Acta Crystallographica Section A: Foundations and Advances最新文献

This article reports the study of algorithms for non-negative matrix factorization (NMF) in various applications involving smoothly varying data such as time or temperature series diffraction data on a dense grid of points. Utilizing the continual nature of the data, a fast two-stage algorithm is developed for highly efficient and accurate NMF. In the first stage, an alternating non-negative least-squares framework is used in combination with the active set method with a warm-start strategy for the solution of subproblems. In the second stage, an interior point method is adopted to accelerate the local convergence. The convergence of the proposed algorithm is proved. The new algorithm is compared with some existing algorithms in benchmark tests using both real-world data and synthetic data. The results demonstrate the advantage of the algorithm in finding high-precision solutions.

A new computational analysis of tilt behaviour in perovskites is presented. This includes the development of a computational program - PALAMEDES - to extract tilt angles and the tilt phase from molecular dynamics simulations. The results are used to generate simulated selected-area electron and neutron diffraction patterns which are compared with experimental patterns for CaTiO₃. The simulations not only reproduced all symmetrically allowed superlattice reflections associated with tilt but also showed local correlations that give rise to symmetrically forbidden reflections and the kinematic origin of diffuse scattering.

Machine learning was employed on the experimental crystal structures of the Cambridge Structural Database (CSD) to derive an intermolecular force field for all available types of atoms (general force field). The obtained pairwise interatomic potentials of the general force field allow for the fast and accurate calculation of intermolecular Gibbs energy. The approach is based on three postulates regarding Gibbs energy: the lattice energy must be below zero, the crystal structure must be a local minimum, and, if available, the experimental and the calculated lattice energy must coincide. The parametrized general force field was then validated regarding these three conditions. First, the experimental lattice energy was compared with the calculated energies. The observed errors were found to be in the order of experimental errors. Second, Gibbs lattice energy was calculated for all structures available in the CSD. Their energy values were found to be below zero in 99.86% of the cases. Finally, 500 random structures were minimized, and the change in density and energy was examined. The mean error in the case of density was below 4.06%, and for energy it was below 5.7%. The obtained general force field calculated Gibbs lattice energies of 259 041 known crystal structures within a few hours. Since Gibbs energy defines the reaction energy, the calculated energy can be used to predict chemical-physical properties of crystals, for instance, the formation of co-crystals, polymorph stability and solubility.

In a quite recent study [Genoni et al. (2017). IUCrJ, 4, 136-146], it was observed that the X-ray restrained wavefunction (XRW) approach allows a more efficient and larger capture of electron correlation effects on the electron density if high-angle reflections are not considered in the calculations. This is due to the occurrence of two concomitant effects when one uses theoretical X-ray diffraction data corresponding to a single-molecule electron density in a large unit cell: (i) the high-angle reflections are generally much more numerous than the low- and medium-angle ones, and (ii) they are already very well described at unrestrained level. Nevertheless, since high-angle data also contain important information that should not be disregarded, it is not advisable to neglect them completely. For this reason, based on the results of the previous investigation, this work introduces a weighting scheme for XRW calculations to up-weight the contribution of low- and medium-angle reflections, and, at the same time, to reasonably down-weight the importance of the high-angle data. The proposed strategy was tested through XRW computations with both theoretical and experimental structure-factor amplitudes. The tests have shown that the new weighting scheme works optimally if it is applied with theoretically generated X-ray diffraction data, while it is not advantageous when traditional experimental X-ray diffraction data (even of very high resolution) are employed. This also led to the conclusion that the use of a specific external parameter λ_J for each resolution range might not be a suitable strategy to adopt in XRW calculations exploiting experimental X-ray data as restraints.

The electron density and thermal motion of diamond are determined at nine temperatures between 100 K and 1000 K via synchrotron powder X-ray diffraction (PXRD) data collected on a high-accuracy detector system. Decoupling of the thermal motion from the thermally smeared electron density is performed via an iterative Wilson-Hansen-Coppens-Rietveld procedure using theoretical static structure factors from density functional theory (DFT) calculations. The thermal motion is found to be harmonic and isotropic in the explored temperature range, and excellent agreement is observed between experimental atomic displacement parameters (ADPs) and those obtained via theoretical harmonic phonon calculations (HPC), even at 1000 K. The Debye temperature of diamond is determined experimentally to be Θ_D = 1883 (35) K. A topological analysis of the electron density explores the temperature dependency of the electron density at the bond critical point. The properties are found to be constant throughout the temperature range. The robustness of the electron density confirms the validity of the crystallographic convolution approximation for diamond in the explored temperature range.

The three fundamental origins of the Lorentz factor for neutron time-of-flight powder diffraction are revisited. A detailed derivation of the Lorentz factor is presented in the context of diffuse scattering modelling in reciprocal space when perfect periodicity is assumed, and the total scattering pattern is constructed in its discrete form - the factor in this case becomes 1/Q² (or d²). Discussion is also presented with respect to practical data reduction where a vanadium measurement is usually taken as the normalization factor (to account for various factors such as detector efficiency), and it is shown that the existence of the Lorentz factor is independent of such a normalization process.

This paper develops geographic style maps containing two-dimensional lattices in all known periodic crystals parameterized by recent complete invariants. Motivated by rigid crystal structures, lattices are considered up to rigid motion and uniform scaling. The resulting space of two-dimensional lattices is a square with identified edges or a punctured sphere. The new continuous maps show all Bravais classes as low-dimensional subspaces, visualize hundreds of thousands of lattices of real crystal structures from the Cambridge Structural Database, and motivate the development of continuous and invariant-based crystallography.

In this first of a series of publications, the X-ray scattering factors for neutral atoms are revisited. Using the recently developed DBSR_HF program [Zatsarinny & Froese Fischer (2016). Comput. Phys. Comm. 202, 287-303] the fully relativistic Dirac-Hartree-Fock ground-state wavefunctions for all atoms with Z = 2-118 (He-Og) have been calculated using the extended average level scheme and including both the Breit interaction correction to the electronic motion due to magnetic and retardation effects, and the Fermi distribution function for the description of the nuclear charge density. The comparison of our wavefunctions with those obtained in several previous studies in terms of the total and orbital (spinor) electronic energies, and a number of local and integrated total and orbital properties, confirmed the quality of the generated wavefunctions. The employed dense radial grid combined with the DBSR_HF's B-spline representation of the relativistic one-electron orbitals allowed for a precise integration of the X-ray scattering factors using a newly developed Fortran program SF. Following the established procedure [Maslen et al. (2006). International Tables for Crystallography, Vol. C, Section 6.1.1, pp. 554-589], the resulting X-ray scattering factors have been interpolated in the 0 ≤ sin θ/λ ≤ 2 Å^-1 and 2 ≤ sin θ/λ ≤ 6 Å^-1 ranges using the recommended analytical functions with both the four- (which is a current convention) and five-term expansions. An exhaustive comparison of the newly generated X-ray scattering factors with the International Union of Crystallography recommended values and those from a number of previous studies showed an overall good agreement and allowed identification of a number of typos and inconsistencies in the recommended quantities. A detailed analysis of the results suggests that the newly derived values may represent an excellent compromise among all the previous studies. The determined conventional interpolating functions for the two sin θ/λ intervals show, on average, the same accuracy as the recommended parametrizations. However, an extension of each expansion by only a single term provides a significant improvement in the accuracy of the interpolated values for an overwhelming majority of the atoms. As such, an updated set of the fully relativistic X-ray scattering factors and the interpolating functions for neutral atoms with Z = 2-118 can be easily incorporated into the existing X-ray diffraction software with only minor modifications. The outcomes of the undertaken research should be of interest to members of the crystallographic community who push the boundaries of the accuracy and precision of X-ray diffraction studies.